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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GTCGTTGCTTCTCGGCGTAGTGGGCACCGATCGATCTCGTCTCCTCCCGAGGCGGCGTGGGCGTGGCGATCGAGGCGAGCCGTTGCATCCGCCCTCACCGgtgagcatccgttactcagccgcaaactatttctccaaagtgacgatctttttcttttttcttctggaatttgcataaccctagctaggttctcttaaagttctggcttaatttgcttaataaccaatcttataagtgagggagggggactaataacagttttttttgttctaaaaaaagttaaatttctgttatgtcag

Basic information

species Oryza sativa
transcript LOC_Os02g21190.2
intron # 1
splice site 5'
intron type U2

Mapped EST sequences

Showing partial alignments of ESTs and genomic sequences. See full alignments


 ATGC     EST sequence
 ATGC     genomic sequence (exon)
 ATGC     genomic sequence (truncated intron)


EST: gi|88571737|gb|CI663110.1|CI663110
EST:     GGCGGCGTGGGCGTGGCGATCGAGGCGAGCCGTTGCATCCGCCCTCACCG                         GTTAGATCCGTCCTCGCTAACCCAACGCCGACGAGAAGTTTGCAGTGCTCT
genomic: GGCGGCGTGGGCGTGGCGATCGAGGCGAGCCGTTGCATCCGCCCTCACCGgtgagcatcc ... gttatgtcagGTTAGATCCGTCCTCGCTAACCCAACGCCGACGAGAAGTTTGCAGTGCTCT
EST: gi|88456198|gb|CI565848.1|CI565848
EST:     GGCGGCGTGGGCGTGGCGATCGAGGCGAGCCGTTGCATCCGCCCTCACCG                         GTTAGATCCGTCCTCGCTAACCCAACGCCGACGAGAAGTTTGCAGTGCTCT
genomic: GGCGGCGTGGGCGTGGCGATCGAGGCGAGCCGTTGCATCCGCCCTCACCGgtgagcatcc ... gttatgtcagGTTAGATCCGTCCTCGCTAACCCAACGCCGACGAGAAGTTTGCAGTGCTCT
EST: gi|88726837|gb|CI750492.1|CI750492
EST:     GGCGGCGTGGGCGTGGCGATCGAGGCGAGCCGTTGCATCCGCCCTCACCG                         GTTAGATCCGTCCTCGCTAACCCAACGCCGACGAGAAGTTTGCAGTGCTCT
genomic: GGCGGCGTGGGCGTGGCGATCGAGGCGAGCCGTTGCATCCGCCCTCACCGgtgagcatcc ... gttatgtcagGTTAGATCCGTCCTCGCTAACCCAACGCCGACGAGAAGTTTGCAGTGCTCT
EST: gi|88722727|gb|CI746237.1|CI746237
EST:     GGCGGCGTGGGCGTGGCGATCGAGGCGAGCCGTTGCATCCGCCCTCACCG                         GTTAGATCCGTCCTCGCTAACCCAACGCCGACGAGAAGTTTGCAGTGCTCT
genomic: GGCGGCGTGGGCGTGGCGATCGAGGCGAGCCGTTGCATCCGCCCTCACCGgtgagcatcc ... gttatgtcagGTTAGATCCGTCCTCGCTAACCCAACGCCGACGAGAAGTTTGCAGTGCTCT
EST: gi|33676405|gb|CF304644.1|CF304644
EST:     GGCGGCGTGGGCGTGGCGATCGAGGCGAGCCGTTGCATCCGCCCTCACCG                         GTTAGATCCGTCCTCGCTAACCCAACGCCGACGAGAAGTTTGCAGTGCTCT
genomic: GGCGGCGTGGGCGTGGCGATCGAGGCGAGCCGTTGCATCCGCCCTCACCGgtgagcatcc ... gttatgtcagGTTAGATCCGTCCTCGCTAACCCAACGCCGACGAGAAGTTTGCAGTGCTCT
EST: gi|88373318|gb|CI614654.1|CI614654
EST:     GGCGGGGTGGGCGTGGCGATCGAGGCGAGCCGTTGCATCCGCCCTCACCG                         GTTAGATCCGTCCTCGCTAACCCAACGCCGACGAGAAGTTTGCAGTGCTCT
genomic: GGCGGCGTGGGCGTGGCGATCGAGGCGAGCCGTTGCATCCGCCCTCACCGgtgagcatcc ... gttatgtcagGTTAGATCCGTCCTCGCTAACCCAACGCCGACGAGAAGTTTGCAGTGCTCT
EST: gi|88720476|gb|CI743775.1|CI743775
EST:     GGCGGCGTGGGCGTGGCGATCGAGGCGAGCCGTTGCATCCGCCCTCACCG                         GTTAGATCCGTCCTCGCTAACCCAACGCCGACGAGAAGTTTGCAGTGCTCT
genomic: GGCGGCGTGGGCGTGGCGATCGAGGCGAGCCGTTGCATCCGCCCTCACCGgtgagcatcc ... gttatgtcagGTTAGATCCGTCCTCGCTAACCCAACGCCGACGAGAAGTTTGCAGTGCTCT
EST: gi|88718793|gb|CI742303.1|CI742303
EST:     GGCGGCGTGGGCGTGGCGATCGAGGCGAGCCGTTGCATCCGCCCTCACCG                         GTTAGATCCGTCCTCGCTAACCCAACGCCGACGAGAAGTTTGCAGTGCTCT
genomic: GGCGGCGTGGGCGTGGCGATCGAGGCGAGCCGTTGCATCCGCCCTCACCGgtgagcatcc ... gttatgtcagGTTAGATCCGTCCTCGCTAACCCAACGCCGACGAGAAGTTTGCAGTGCTCT
EST: gi|88454353|gb|CI569925.1|CI569925
EST:     GGCGGCGTGGGCGTGGCGATCGAGGCGAGCCGTTGCATCCGCCCTCACCG                         GTTAGATCCGTCCTCGCTAACCCAACGCCGACGAGAAGTTTGCAGTGCTCT
genomic: GGCGGCGTGGGCGTGGCGATCGAGGCGAGCCGTTGCATCCGCCCTCACCGgtgagcatcc ... gttatgtcagGTTAGATCCGTCCTCGCTAACCCAACGCCGACGAGAAGTTTGCAGTGCTCT
EST: gi|88692210|gb|CI735785.1|CI735785
EST:     GGCGGCGTGGGCGTGGCGATCGAGGCGAGCCGTTGCATCCGCCCTCACCG                         GTTAGATCCGTCCTCGCTAACCCAACGCCGACGAGAAGTTTGCAGTGCTCT
genomic: GGCGGCGTGGGCGTGGCGATCGAGGCGAGCCGTTGCATCCGCCCTCACCGgtgagcatcc ... gttatgtcagGTTAGATCCGTCCTCGCTAACCCAACGCCGACGAGAAGTTTGCAGTGCTCT
EST: gi|88357109|gb|CI615996.1|CI615996
EST:     GGCGGCGTGGGCGTGGCGATCGAGGCGAGCCGTTGCATCCGCCCTCACCG                         GTTAGATCCGTCCTCGCTAACCCAACGCCGACGAGAAGTTTGCAGTGCTCT
genomic: GGCGGCGTGGGCGTGGCGATCGAGGCGAGCCGTTGCATCCGCCCTCACCGgtgagcatcc ... gttatgtcagGTTAGATCCGTCCTCGCTAACCCAACGCCGACGAGAAGTTTGCAGTGCTCT
EST: gi|88302370|gb|CI668216.1|CI668216
EST:     GGCGGCGTGGGCGTGGCGATCGAGGCGAGCCGTTGCATCCGCCCTCACCG                         GTTAGATCCGTCCTCGCTAACCCAACGCCGACGAGAAGTNTGCAGTGCTCT
genomic: GGCGGCGTGGGCGTGGCGATCGAGGCGAGCCGTTGCATCCGCCCTCACCGgtgagcatcc ... gttatgtcagGTTAGATCCGTCCTCGCTAACCCAACGCCGACGAGAAGTTTGCAGTGCTCT
EST: gi|88576822|gb|CI673349.1|CI673349
EST:     GGCGGCGTGGGCGTGGCGATCGAGGCGAGCCGTTGCATCCGCCCTCACCG                         GTTAGATCCGTCCTCGCTAACCCAACGCCGACGAGAAGTTTGCAGTGCTCT
genomic: GGCGGCGTGGGCGTGGCGATCGAGGCGAGCCGTTGCATCCGCCCTCACCGgtgagcatcc ... gttatgtcagGTTAGATCCGTCCTCGCTAACCCAACGCCGACGAGAAGTTTGCAGTGCTCT
EST: gi|88354559|gb|CI678596.1|CI678596
EST:     GGCGGCGTGGGCGTGGCGATCGAGGCGAGCCGTTGCATCCGCCCTCACCG                         GTTAGATCCGTCCTCGCTAACCCAACGCCGACGAGAAGTTTGCAGTGCTCT
genomic: GGCGGCGTGGGCGTGGCGATCGAGGCGAGCCGTTGCATCCGCCCTCACCGgtgagcatcc ... gttatgtcagGTTAGATCCGTCCTCGCTAACCCAACGCCGACGAGAAGTTTGCAGTGCTCT
EST: gi|88387120|gb|CI577906.1|CI577906
EST:     GGCGGCGTGGGCGTGGCGATCGAGGCGAGCCGTTGCATCCGCCCTCACCG                         GTTAGATCCGTCCTCGCTAACCCAACGCCGACGAGAAGTTTGCAGTGCTCT
genomic: GGCGGCGTGGGCGTGGCGATCGAGGCGAGCCGTTGCATCCGCCCTCACCGgtgagcatcc ... gttatgtcagGTTAGATCCGTCCTCGCTAACCCAACGCCGACGAGAAGTTTGCAGTGCTCT
EST: gi|88731027|gb|CI754640.1|CI754640
EST:     GGCGGCGTGGGCGTGGCGATCGAGGCGAGCCGTTGCATCCGCCCTCACCG                         GTTAGATCCGTCCTCGCTAACCCAACGCCGACGAGAAGTTTGCAGTGCTCT
genomic: GGCGGCGTGGGCGTGGCGATCGAGGCGAGCCGTTGCATCCGCCCTCACCGgtgagcatcc ... gttatgtcagGTTAGATCCGTCCTCGCTAACCCAACGCCGACGAGAAGTTTGCAGTGCTCT
EST: gi|88447518|gb|CI584633.1|CI584633
EST:     GGCGGCGTGGGCGTGGCGATCGAGGCGAGCCGTTGCATCCGCCCTCACCG                         GTTAGATCCGTCCTCGCTAACCCAACGCCGACGAGAAGTTTGCAGTGCTCT
genomic: GGCGGCGTGGGCGTGGCGATCGAGGCGAGCCGTTGCATCCGCCCTCACCGgtgagcatcc ... gttatgtcagGTTAGATCCGTCCTCGCTAACCCAACGCCGACGAGAAGTTTGCAGTGCTCT
EST: gi|88570056|gb|CI661231.1|CI661231
EST:     GGCGGCGTGGGCGTGGCGATCGAGGCGAGCCGTTGCATCCGCCCTCACCG                         GTTAGATCCGTCCTCGCTAACCCAACGCCGACGAGAAGTTTGCAGTGCTCT
genomic: GGCGGCGTGGGCGTGGCGATCGAGGCGAGCCGTTGCATCCGCCCTCACCGgtgagcatcc ... gttatgtcagGTTAGATCCGTCCTCGCTAACCCAACGCCGACGAGAAGTTTGCAGTGCTCT

RNA-Seq data


 ATGC   Supported by RNA-Seq exonic block that spans over the splice site

 atgs   Truncated intron sequence

Each block is as long as the maximal overhang of any read spanning the junction.
The score is the number of alignments spanning the junction.


Found data for 1 RNA-Seqlibrary.


Block sizes: 27 (upstream exon), 64 (downstream exon)
Score: 4

GTCGTTGCTTCTCGGCGTAGTGGGCACCGATCGATCTCGTCTCCTCCCGAGGCGGCGTGGGCGTGGCGATCGAGGCGAGCCGTTGCATCCGCCCTCACCGgtgagcatcc ... gttatgtcagGTTAGATCCGTCCTCGCTAACCCAACGCCGACGAGAAGTTTGCAGTGCTCTAGTATGTGAAACGGATCGATTTCCATTTGAGCAGCAGCAACTGCTGCTG




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